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protocols::membrane::MPLipidAccessibility Class Reference

Mover that computes which residues are lipid accessible and puts that information into the B-factors: 50 is lipid accessible, 0 is lipid INaccessible. More...

#include <MPLipidAccessibility.hh>

Inheritance diagram for protocols::membrane::MPLipidAccessibility:
Inheritance graph
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Public Member Functions

 MPLipidAccessibility ()
 Constructors ///. More...
 
 ~MPLipidAccessibility () override
 Copy constructor (not needed unless you need deep copies) More...
 
void apply (core::pose::Pose &pose) override
 Mover Methods ///. More...
 
void show (std::ostream &output=std::cout) const override
 Show the contents of the Mover. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 Get the name of the Mover. More...
 
protocols::moves::MoverOP fresh_instance () const override
 required in the context of the parser/scripting scheme More...
 
protocols::moves::MoverOP clone () const override
 required in the context of the parser/scripting scheme More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
core::Real get_angle_cutoff () const
 Get Methods ///. More...
 
core::Real get_slice_width () const
 get slice width More...
 
void set_slice_width (core::Real width)
 Set slice width via commandline More...
 
core::Real get_shell_radius () const
 get shell radius More...
 
core::Real get_dist_cutoff () const
 get dist cutoff More...
 
bool get_tm_alpha () const
 get tm_alpha More...
 
bool is_alpha_helical () const
 Is this an alpha helical protein? (no >7 exception) More...
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual MoverOP create ()
 
MoverCOP get_self_ptr () const
 
MoverOP get_self_ptr ()
 
MoverCAP get_self_weak_ptr () const
 
MoverAP get_self_weak_ptr ()
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
virtual void test_move (Pose &pose)
 : Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...
 
virtual bool reinitialize_for_each_job () const
 Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...
 
virtual bool reinitialize_for_new_input () const
 Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...
 
MoverStatus get_last_move_status () const
 end parser interface, start Job Distributor interface///////////// More...
 
void reset_status ()
 resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...
 
virtual core::pose::PoseOP get_additional_output ()
 Mechanism by which a mover may return multiple output poses from a single input pose. More...
 
void set_type (std::string const &setting)
 Set the 'type' string. More...
 
std::string get_type () const
 
void type (const std::string &type_in)
 Set the 'type' string. More...
 
std::string const & type () const
 Get the set 'type' string. More...
 
virtual void set_input_pose (PoseCOP pose)
 setter for poses contained for rms More...
 
virtual void set_native_pose (PoseCOP pose)
 setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...
 
PoseCOP get_input_pose () const
 
PoseCOP get_native_pose () const
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 
virtual void set_current_tag (std::string const &new_tag)
 
std::string get_current_tag () const
 A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...
 
virtual core::Real last_proposal_density_ratio ()
 
virtual void clear_info ()
 Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...
 
virtual Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Static Public Member Functions

static std::string mover_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
- Static Public Member Functions inherited from protocols::moves::Mover
static std::string name ()
 
static void register_options ()
 Overload this static method if you access options within the mover. More...
 

Private Member Functions

void set_defaults ()
 set defaults More...
 
void register_options ()
 Register Options from Command Line. More...
 
void init_from_cmd ()
 Initialize from commandline. More...
 
void finalize_setup (Pose &pose)
 finalize setup More...
 
bool protein_in_membrane (Pose &pose)
 check whether protein is in membrane More...
 
void fill_up_slices (Pose &pose)
 fill up slice arrays with protein data More...
 
void compute_slice_com ()
 compute slice COM More...
 

Private Attributes

core::Real angle_cutoff_
 original data from first implementation More...
 
core::Real slice_width_
 
core::Real shell_radius_
 
core::Real dist_cutoff_
 
bool tm_alpha_
 
bool is_alpha_helical_
 
utility::vector1
< utility::vector1< core::Size > > 
resi_
 
utility::vector1
< utility::vector1
< core::Vector > > 
ca_coord_
 
utility::vector1
< utility::vector1
< core::Vector > > 
cb_coord_
 
utility::vector1< core::Vectorslice_com_
 
utility::vector1< core::Realslice_zmin_
 
utility::vector1
< utility::vector1< core::Real > > 
per_atom_lipid_accessibility_
 

Additional Inherited Members

- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP TagCOP
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef std::list< std::string > Strings
 
- Protected Member Functions inherited from protocols::moves::Mover
void set_last_move_status (MoverStatus status)
 nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...
 

Detailed Description

Mover that computes which residues are lipid accessible and puts that information into the B-factors: 50 is lipid accessible, 0 is lipid INaccessible.

Constructor & Destructor Documentation

protocols::membrane::MPLipidAccessibility::MPLipidAccessibility ( )

Constructors ///.

Default constructor

References init_from_cmd(), register_options(), and set_defaults().

protocols::membrane::MPLipidAccessibility::~MPLipidAccessibility ( )
overridedefault

Copy constructor (not needed unless you need deep copies)

Destructor (important for properly forward-declaring smart-pointer members)

Member Function Documentation

void protocols::membrane::MPLipidAccessibility::apply ( core::pose::Pose pose)
overridevirtual
protocols::moves::MoverOP protocols::membrane::MPLipidAccessibility::clone ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

void protocols::membrane::MPLipidAccessibility::compute_slice_com ( )
private

compute slice COM

References ca_coord_, protocols::membrane::com(), resi_, slice_com_, slice_zmin_, and protocols::TR().

Referenced by fill_up_slices().

void protocols::membrane::MPLipidAccessibility::fill_up_slices ( Pose pose)
private
void protocols::membrane::MPLipidAccessibility::finalize_setup ( Pose pose)
private
protocols::moves::MoverOP protocols::membrane::MPLipidAccessibility::fresh_instance ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

core::Real protocols::membrane::MPLipidAccessibility::get_angle_cutoff ( ) const

Get Methods ///.

get angle cutoff

References angle_cutoff_.

core::Real protocols::membrane::MPLipidAccessibility::get_dist_cutoff ( ) const

get dist cutoff

References dist_cutoff_.

std::string protocols::membrane::MPLipidAccessibility::get_name ( ) const
overridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

References mover_name().

core::Real protocols::membrane::MPLipidAccessibility::get_shell_radius ( ) const

get shell radius

References shell_radius_.

core::Real protocols::membrane::MPLipidAccessibility::get_slice_width ( ) const

get slice width

References slice_width_.

bool protocols::membrane::MPLipidAccessibility::get_tm_alpha ( ) const

get tm_alpha

References tm_alpha_.

void protocols::membrane::MPLipidAccessibility::init_from_cmd ( )
private

Initialize from commandline.

References angle_cutoff_, dist_cutoff_, shell_radius_, slice_width_, and tm_alpha_.

Referenced by MPLipidAccessibility().

bool protocols::membrane::MPLipidAccessibility::is_alpha_helical ( ) const

Is this an alpha helical protein? (no >7 exception)

References is_alpha_helical_.

std::string protocols::membrane::MPLipidAccessibility::mover_name ( )
static
void protocols::membrane::MPLipidAccessibility::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual

Get the name of the Mover.

Rosetta Scripts Support ///.

Rosetta Scripts Support /// parse XML tag (to use this Mover in Rosetta Scripts)

parse XML tag (to use this Mover in Rosetta Scripts)

Reimplemented from protocols::moves::Mover.

References angle_cutoff_, dist_cutoff_, shell_radius_, slice_width_, and tm_alpha_.

bool protocols::membrane::MPLipidAccessibility::protein_in_membrane ( Pose pose)
private

check whether protein is in membrane

check whether protein is transformed into membrane

References core::conformation::Residue::name3(), core::pose::nres_protein(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by finalize_setup().

void protocols::membrane::MPLipidAccessibility::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::membrane::MPLipidAccessibility::register_options ( )
private

Register Options from Command Line.

Referenced by MPLipidAccessibility().

void protocols::membrane::MPLipidAccessibility::set_defaults ( )
private

set defaults

private methods ///

set defaults

References angle_cutoff_, dist_cutoff_, is_alpha_helical_, shell_radius_, slice_width_, and tm_alpha_.

Referenced by MPLipidAccessibility().

void protocols::membrane::MPLipidAccessibility::set_slice_width ( core::Real  width)

Set slice width via commandline

set slice width (should be an integer multiple of membrane thickness)

References slice_width_.

void protocols::membrane::MPLipidAccessibility::show ( std::ostream &  output = std::cout) const
overridevirtual

Show the contents of the Mover.

Reimplemented from protocols::moves::Mover.

References protocols::moves::Mover::show().

Member Data Documentation

core::Real protocols::membrane::MPLipidAccessibility::angle_cutoff_
private

original data from first implementation

Referenced by apply(), finalize_setup(), get_angle_cutoff(), init_from_cmd(), parse_my_tag(), and set_defaults().

utility::vector1< utility::vector1< core::Vector > > protocols::membrane::MPLipidAccessibility::ca_coord_
private
utility::vector1< utility::vector1< core::Vector > > protocols::membrane::MPLipidAccessibility::cb_coord_
private

Referenced by apply(), and fill_up_slices().

core::Real protocols::membrane::MPLipidAccessibility::dist_cutoff_
private
bool protocols::membrane::MPLipidAccessibility::is_alpha_helical_
private
utility::vector1< utility::vector1< core::Real > > protocols::membrane::MPLipidAccessibility::per_atom_lipid_accessibility_
private
utility::vector1< utility::vector1< core::Size > > protocols::membrane::MPLipidAccessibility::resi_
private
core::Real protocols::membrane::MPLipidAccessibility::shell_radius_
private
utility::vector1< core::Vector > protocols::membrane::MPLipidAccessibility::slice_com_
private

Referenced by apply(), and compute_slice_com().

core::Real protocols::membrane::MPLipidAccessibility::slice_width_
private
utility::vector1< core::Real > protocols::membrane::MPLipidAccessibility::slice_zmin_
private
bool protocols::membrane::MPLipidAccessibility::tm_alpha_
private

The documentation for this class was generated from the following files: